Will have to disagree with you on a few things there Mal.
Firstly, a 3" mandrel exhaust is perfect for the BPT engine in standard form. Being a turbo efi engine, it doesn't really care how big it is, and I've proved that there is a difference from just going from a 2.5" muffler up to a 3" which is the same size as the rest of my system. The difference was boost coming on alot quicker and also increasing power in top end. I'd never go back to a 2.5" system.
Boost cut on the GTX ECU is 14.7psi. With running a 3" system with a pod filter you will find that you'll run boost around 10-11psi @ 6000rpm. In the lower rev range when you plant it you boost will be the standard 7-8psi and then go up with rpm. Better known as boost creep or overboost. Porting the wastegate didn't solve the problem for me either...although I don't call that amount of creep a problem because it never goes over it. I've only know one other person who has had problems with running a 3" exhaust...he fixed his problem by changing the position of the wastegate pressure feed to before the intercooler instead of after it like the GTX setup is.
Nate, you've got to upgrade alot your engine and control system than just ECU for put on a larger turbo. As the guys have already said, go slow and you'll never regret doing the conversion. Every little mod that you do to this engine, it will show you a difference...that's what I have loved so much about doing the GTX conversion firstly on my laser and now continuing on my astina. Upgrade as you go, eg, Fuel pressure reg, boost increase, intercooler, fuel pump, and then go the turbo and ecu.
My 2c
ROB.